Abstract. This study addresses the challenges inherent in preserving archaeological waterlogged wood, which is prone to deformation and decay if not stabilized immediately after recovery. Conventional preservation methods, such as impregnation with polyethylene glycol (PEG) solutions, often result in undesirable dimensional changes. To obtain exact spatio-temporal information on the deformations during the conservation process, a photogrammetric monitoring system, utilizing a stereo camera facing from air into the liquid, attached to an automated biaxial measurement unit is proposed. Special target heads were developed and attached to the wood to provide deformation points. Refraction correction was applied to the imaging model by ray tracing, and indirect flat lighting was used to mitigate turbidity. The system observed logs from a wooden track from the first century, subject to conservation. Subject of investigation were the influence of refraction negligence and scale definition in a bundle geometry, similar to bathymetric aerial setups. Results show that refraction correction is imperative for good results. Furthermore, scale definition with highly accurately determined scale bars and inclusion of relative orientation constraints provide further accuracy improvements.